GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutF in Pseudomonas fluorescens FW300-N2E3

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate AO353_12235 AO353_12235 N-formimino-L-glutamate deiminase

Query= reanno::pseudo3_N2E3:AO353_12235
         (454 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12235
          Length = 454

 Score =  923 bits (2386), Expect = 0.0
 Identities = 454/454 (100%), Positives = 454/454 (100%)

Query: 1   MSAFFAERALLPSGWANNVRLEVSADGLLTHIQADASAEGAERLSGPLLPGMPNLHSHAF 60
           MSAFFAERALLPSGWANNVRLEVSADGLLTHIQADASAEGAERLSGPLLPGMPNLHSHAF
Sbjct: 1   MSAFFAERALLPSGWANNVRLEVSADGLLTHIQADASAEGAERLSGPLLPGMPNLHSHAF 60

Query: 61  QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPEQLGIIARQLYIEMLKAGYTSVAEFH 120
           QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPEQLGIIARQLYIEMLKAGYTSVAEFH
Sbjct: 61  QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPEQLGIIARQLYIEMLKAGYTSVAEFH 120

Query: 121 YVHHDHNGHPYADPAELSLQISQAASASGIGLTLLPVLYSHSGFGGLAPNEGQRRFINST 180
           YVHHDHNGHPYADPAELSLQISQAASASGIGLTLLPVLYSHSGFGGLAPNEGQRRFINST
Sbjct: 121 YVHHDHNGHPYADPAELSLQISQAASASGIGLTLLPVLYSHSGFGGLAPNEGQRRFINST 180

Query: 181 ENYLKLQARLQPLLAQQPAQQLGLCFHSLRAVTPQQISEVLAASDKHCPVHIHIAEQQKE 240
           ENYLKLQARLQPLLAQQPAQQLGLCFHSLRAVTPQQISEVLAASDKHCPVHIHIAEQQKE
Sbjct: 181 ENYLKLQARLQPLLAQQPAQQLGLCFHSLRAVTPQQISEVLAASDKHCPVHIHIAEQQKE 240

Query: 241 VDDCLIWSGRRPLQWLYENTDVDQRWCLVHATHANPEEVSLMAKSRAIAGLCLTTEANLG 300
           VDDCLIWSGRRPLQWLYENTDVDQRWCLVHATHANPEEVSLMAKSRAIAGLCLTTEANLG
Sbjct: 241 VDDCLIWSGRRPLQWLYENTDVDQRWCLVHATHANPEEVSLMAKSRAIAGLCLTTEANLG 300

Query: 301 DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYGADQPMVGRT 360
           DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYGADQPMVGRT
Sbjct: 301 DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYGADQPMVGRT 360

Query: 361 LYDAALDGGAQALGQPIGALEVGKRADWLVLDGNDPYLATASGDGILNRWLFAGGDRQVR 420
           LYDAALDGGAQALGQPIGALEVGKRADWLVLDGNDPYLATASGDGILNRWLFAGGDRQVR
Sbjct: 361 LYDAALDGGAQALGQPIGALEVGKRADWLVLDGNDPYLATASGDGILNRWLFAGGDRQVR 420

Query: 421 DVLVNGKWVVRDGHHAGEEDSNRAFTQVLRELLG 454
           DVLVNGKWVVRDGHHAGEEDSNRAFTQVLRELLG
Sbjct: 421 DVLVNGKWVVRDGHHAGEEDSNRAFTQVLRELLG 454


Lambda     K      H
   0.319    0.136    0.417 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 846
Number of extensions: 17
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 454
Length of database: 454
Length adjustment: 33
Effective length of query: 421
Effective length of database: 421
Effective search space:   177241
Effective search space used:   177241
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate AO353_12235 AO353_12235 (N-formimino-L-glutamate deiminase)
to HMM TIGR02022 (hutF: formiminoglutamate deiminase (EC 3.5.3.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.1566.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1566.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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